with the EOL of JavaFX 1.x nearing, we have to migrate a large FX script application codebase to JavaFX 2.1. Visage is not an option for us, as the future of the project is unclear at this point. So we're looking at the tedious task of manually rewriting the application UI.

I've found surprisingly few information and no official statements about the tooling and documentation supporting the migration.
Reading this forum makes me believe that there are no publicly available tools for completely or partially automating the migration. Am I missing something here?

Further, I've failed to locate a comprehensible migration guide or documentation about the best practices of the migration.
Even the JavaFX site http://www.oracle.com/technetwork/java/javafx/overview/index.html does not seem to mention any details.

I would be very thankful for your advice or pointers to relevant documentation.

Visage is not an option for us, as the future of the project is unclear at this point.

IMO, not using Visage at this stage (and perhaps ever) is a good idea.

for your advice or pointers to relevant documentation.

Just start the manual conversion process - as a side benefit, you will learn the JavaFX 2 platform.
Hopefully the task won't prove too tedious. IMO JavaFX 2 is quite fun to use even for a converted project, but opinions may vary.
Css should convert without too much issue. NetBeans 7.2 has parses JavaFX 2.2 css files I believe, so load your css up in NetBeans and it should notify you of syntax errors or mismatched tags at least.
Conversion of FXD to FXML probably will probably be pretty straightforward. Controls and Layouts differ somewhat between the 1.x and 2.x versions, so in addition to changing document format you will also need to rewrite some of the content to adapt to the controls and layouts for 2.x. You could do this conversion by hand or you could use SceneBuilder to visually layout your UI from scratch and then generate the FXML from SceneBuilder.
Conversion of general code will be some work.